Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate BPHYT_RS22700 BPHYT_RS22700 FAD-dependent oxidoreductase
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >FitnessBrowser__BFirm:BPHYT_RS22700 Length = 426 Score = 252 bits (644), Expect = 1e-71 Identities = 149/412 (36%), Positives = 220/412 (53%), Gaps = 6/412 (1%) Query: 8 ESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFK-VTVLEAAKVGFG 66 +S+Y A+ L +VCVIG G GLS+AL L E G VTVLEA +VGFG Sbjct: 2 QSFYEATVTRSSAYAPLAGRRAANVCVIGGGLAGLSTALGLAERGVADVTVLEARQVGFG 61 Query: 67 ASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDGG 126 ASGRNGG + YS D + +++G +A+ L + + ++R+R+A+Y I CD D G Sbjct: 62 ASGRNGGFVFGGYSLDCADLLKTLGAVRARELYTLTTDAVDLMRKRIARYHIDCDATDAG 121 Query: 127 VFAALTAKQMGHLESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSGGHIHPL 186 V A + LESQ+RL + E + +++ + Y G+ + + H HPL Sbjct: 122 VILANWFDEPARLESQRRLMRDSFGVEWEPVAAQQLASQLKTRRYHSGLFERNAFHFHPL 181 Query: 187 NLALGEAAAVESLGGVIYEQSPAVRIER-GASPVVHTPQGKVRAKFIIVAGNAYLGNLVP 245 LG A A G I+E SP VR+ER GA VVHT G + A+ +++AG Y + P Sbjct: 182 KYVLGVANAAAHAGVQIHEDSPVVRLERDGAGFVVHTQHGVLDARHVVMAGGGYARRVYP 241 Query: 246 ELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGGGVVY 305 + +P T V+ATEPLG L + + D + DYYR D R+++GG + Sbjct: 242 RVERAVLPIATYVMATEPLGARL-QDAIDTRAAIYDTRFAFDYYRPLPDTRILWGGRISV 300 Query: 306 GARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYYSQGCS 365 R+P I ++R +LK +PQL V+IDYAW G ++PQ+GR D ++Y+ G Sbjct: 301 RDREPEVIARLLRRDLLKVYPQLHGVRIDYAWGGLMSYARHKMPQIGRSADGVWYAVGFG 360 Query: 366 GHGVTYTHLAGKVLAEALRGQ---AERFDAFADLPHYPFPGGQLLRTPFAAM 414 GHG+ T ++G++LA A+ G+ E F +F P Y G + + AM Sbjct: 361 GHGMAPTTVSGELLAAAIAGERPVPEAFASFGLTPAYGALGLAAAQLTYTAM 412 Lambda K H 0.320 0.139 0.421 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 506 Number of extensions: 23 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 427 Length of database: 426 Length adjustment: 32 Effective length of query: 395 Effective length of database: 394 Effective search space: 155630 Effective search space used: 155630 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory